RetrogeneDB ID: retro_hsap_738

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 10:122114215..122114695(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000220842
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPL21
• Ensembl ID: ENSG00000122026
• Aliases: RPL21, L21
• Description: ribosomal protein L21 [Source:HGNC Symbol;Acc:10313]

Sequence

>retro_hsap_738
ATGACGAACACAAAGGGAAAGAGGAGAGGCACCCGATATATGTTCTCTAGGCCTTTTAGAAAACATGGAGTTGTTCCTTT
GGCCACATATATGCGAATCTATAAGAAAGGTGATATTGTAGACATCAAGGGAATGGGTACTGTTCAAAAAGGAATGCCCC
ACAAGTGTTACCATGGCAAAACTGGAAGAGTCTACAATGTTACCCAGCATGCTGTTGGCATTGTTGTAAACAAACAAGTT
AAGGGCAAGATTCTTGCCAAGAGAATTAATGTGCGTATTGAGCACATTAAGCACTCTAAGAGCCGAGATAGCTTCCTGAA
ACGTGTGAAGGAAAATGATCAGAAAAAGAAAGAAGCCAAAGAGAAAGGTACCTGGGTTCAACTAAAGCGCCAGCCTGCTC
CACCCAGAGAAGCACACTTTGTGAGAACCAATGGGAAGGAGCCTGAGCTGCTGGAACCTATTCCCTATGAATTCATGGCA

Alignment

ORF - retro_hsap_738 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100. %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTNTKGKRRGTRYMFSRPFRKHGVVPLATYMRIYKKGDIVDIKGMGTVQKGMPHKCYHGKTGRVYNVTQH
          MTNTKGKRRGTRYMFSRPFRKHGVVPLATYMRIYKKGDIVDIKGMGTVQKGMPHKCYHGKTGRVYNVTQH
Retrocopy MTNTKGKRRGTRYMFSRPFRKHGVVPLATYMRIYKKGDIVDIKGMGTVQKGMPHKCYHGKTGRVYNVTQH

Parental  AVGIVVNKQVKGKILAKRINVRIEHIKHSKSRDSFLKRVKENDQKKKEAKEKGTWVQLKRQPAPPREAHF
          AVGIVVNKQVKGKILAKRINVRIEHIKHSKSRDSFLKRVKENDQKKKEAKEKGTWVQLKRQPAPPREAHF
Retrocopy AVGIVVNKQVKGKILAKRINVRIEHIKHSKSRDSFLKRVKENDQKKKEAKEKGTWVQLKRQPAPPREAHF

Parental  VRTNGKEPELLEPIPYEFMA
          VRTNGKEPELLEPIPYEFMA
Retrocopy VRTNGKEPELLEPIPYEFMA

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
bodymap2_adipose	0.87 RPM	80.68 RPM
bodymap2_adrenal	1.08 RPM	121.12 RPM
bodymap2_brain	0.09 RPM	35.89 RPM
bodymap2_breast	0.66 RPM	60.37 RPM
bodymap2_colon	2.05 RPM	99.58 RPM
bodymap2_heart	0.02 RPM	111.91 RPM
bodymap2_kidney	0.21 RPM	84.83 RPM
bodymap2_liver	0.13 RPM	89.65 RPM
bodymap2_lung	0.74 RPM	422.43 RPM
bodymap2_lymph_node	0.80 RPM	336.42 RPM
bodymap2_ovary	0.98 RPM	157.01 RPM
bodymap2_prostate	1.47 RPM	418.56 RPM
bodymap2_skeletal_muscle	0.09 RPM	150.89 RPM
bodymap2_testis	0.47 RPM	54.92 RPM
bodymap2_thyroid	0.34 RPM	74.87 RPM
bodymap2_white_blood_cells	0.53 RPM	422.68 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_738 was not detected

EST

No EST(s) were mapped for retro_hsap_738 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_1798	779 libraries	876 libraries	171 libraries	1 library	2 libraries

The graphical summary, for retro_hsap_738 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_hsap_738 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_738 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 295 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001648	5 retrocopies	retro_btau_1383, retro_btau_194, retro_btau_209, retro_btau_93, retro_btau_976,
Homo sapiens	ENSG00000122026	105 retrocopies	retro_hsap_1007, retro_hsap_1011, retro_hsap_1019, retro_hsap_1032, retro_hsap_1040, retro_hsap_1099, retro_hsap_1107, retro_hsap_1213, retro_hsap_1218, retro_hsap_122, retro_hsap_1280, retro_hsap_1288, retro_hsap_1298, retro_hsap_1379, retro_hsap_1381, retro_hsap_1419, retro_hsap_143, retro_hsap_1430, retro_hsap_1446, retro_hsap_1453, retro_hsap_1505, retro_hsap_1576, retro_hsap_1578, retro_hsap_160, retro_hsap_1600, retro_hsap_1663, retro_hsap_1712, retro_hsap_1723, retro_hsap_1734, retro_hsap_1757, retro_hsap_1805, retro_hsap_1842, retro_hsap_1886, retro_hsap_1904, retro_hsap_1920, retro_hsap_2050, retro_hsap_2088, retro_hsap_2109, retro_hsap_2153, retro_hsap_2178, retro_hsap_2221, retro_hsap_2245, retro_hsap_2258, retro_hsap_2266, retro_hsap_2357, retro_hsap_2442, retro_hsap_252, retro_hsap_2625, retro_hsap_2635, retro_hsap_2655, retro_hsap_2716, retro_hsap_2855, retro_hsap_2876, retro_hsap_2916, retro_hsap_2937, retro_hsap_3037, retro_hsap_3039, retro_hsap_3091, retro_hsap_3094, retro_hsap_3119, retro_hsap_3160, retro_hsap_3185, retro_hsap_3264, retro_hsap_3304, retro_hsap_3375, retro_hsap_3429, retro_hsap_3435, retro_hsap_3521, retro_hsap_3555, retro_hsap_3558, retro_hsap_362, retro_hsap_3628, retro_hsap_3658, retro_hsap_3662, retro_hsap_367, retro_hsap_3688, retro_hsap_3694, retro_hsap_3705, retro_hsap_3747, retro_hsap_3764, retro_hsap_381, retro_hsap_3911, retro_hsap_3945, retro_hsap_3955, retro_hsap_4092, retro_hsap_4193, retro_hsap_424, retro_hsap_4276, retro_hsap_4283, retro_hsap_4286, retro_hsap_4302, retro_hsap_4713, retro_hsap_4733, retro_hsap_496, retro_hsap_503, retro_hsap_563, retro_hsap_573, retro_hsap_582, retro_hsap_626, retro_hsap_654, retro_hsap_738 , retro_hsap_752, retro_hsap_819, retro_hsap_900, retro_hsap_965,
Latimeria chalumnae	ENSLACG00000012678	1 retrocopy	retro_lcha_32,
Loxodonta africana	ENSLAFG00000003677	11 retrocopies	retro_lafr_1167, retro_lafr_308, retro_lafr_331, retro_lafr_583, retro_lafr_63, retro_lafr_652, retro_lafr_738, retro_lafr_740, retro_lafr_856, retro_lafr_89, retro_lafr_97,
Myotis lucifugus	ENSMLUG00000010093	46 retrocopies	retro_mluc_1066, retro_mluc_1079, retro_mluc_1138, retro_mluc_1164, retro_mluc_1171, retro_mluc_1219, retro_mluc_1274, retro_mluc_1279, retro_mluc_1307, retro_mluc_1323, retro_mluc_1379, retro_mluc_1382, retro_mluc_1409, retro_mluc_1413, retro_mluc_1469, retro_mluc_1481, retro_mluc_1525, retro_mluc_162, retro_mluc_1647, retro_mluc_1753, retro_mluc_1803, retro_mluc_1849, retro_mluc_1862, retro_mluc_1929, retro_mluc_1969, retro_mluc_1981, retro_mluc_2044, retro_mluc_2077, retro_mluc_2109, retro_mluc_2121, retro_mluc_2212, retro_mluc_230, retro_mluc_2335, retro_mluc_2338, retro_mluc_2436, retro_mluc_2592, retro_mluc_27, retro_mluc_279, retro_mluc_360, retro_mluc_503, retro_mluc_554, retro_mluc_620, retro_mluc_631, retro_mluc_806, retro_mluc_961, retro_mluc_97,
Monodelphis domestica	ENSMODG00000008923	1 retrocopy	retro_mdom_156,
Mus musculus	ENSMUSG00000041453	101 retrocopies	retro_mmus_1012, retro_mmus_1046, retro_mmus_1057, retro_mmus_1083, retro_mmus_1123, retro_mmus_1199, retro_mmus_1287, retro_mmus_1354, retro_mmus_1461, retro_mmus_1475, retro_mmus_1529, retro_mmus_1561, retro_mmus_1572, retro_mmus_1596, retro_mmus_1617, retro_mmus_1641, retro_mmus_1644, retro_mmus_17, retro_mmus_1714, retro_mmus_1739, retro_mmus_1762, retro_mmus_1797, retro_mmus_1848, retro_mmus_1860, retro_mmus_1862, retro_mmus_1875, retro_mmus_1897, retro_mmus_1915, retro_mmus_1931, retro_mmus_1936, retro_mmus_1994, retro_mmus_2042, retro_mmus_2049, retro_mmus_2101, retro_mmus_2130, retro_mmus_2176, retro_mmus_2179, retro_mmus_2185, retro_mmus_2214, retro_mmus_2233, retro_mmus_2237, retro_mmus_2238, retro_mmus_2279, retro_mmus_2309, retro_mmus_2312, retro_mmus_2335, retro_mmus_2344, retro_mmus_2395, retro_mmus_2447, retro_mmus_2517, retro_mmus_2567, retro_mmus_2585, retro_mmus_2598, retro_mmus_266, retro_mmus_2662, retro_mmus_2698, retro_mmus_2707, retro_mmus_2778, retro_mmus_2808, retro_mmus_2853, retro_mmus_2874, retro_mmus_2945, retro_mmus_2980, retro_mmus_3035, retro_mmus_3055, retro_mmus_3085, retro_mmus_3103, retro_mmus_3112, retro_mmus_3220, retro_mmus_3252, retro_mmus_3261, retro_mmus_3295, retro_mmus_3318, retro_mmus_3328, retro_mmus_333, retro_mmus_3341, retro_mmus_3446, retro_mmus_3545, retro_mmus_3581, retro_mmus_3712, retro_mmus_397, retro_mmus_400, retro_mmus_401, retro_mmus_598, retro_mmus_601, retro_mmus_606, retro_mmus_663, retro_mmus_734, retro_mmus_735, retro_mmus_758, retro_mmus_782, retro_mmus_806, retro_mmus_835, retro_mmus_862, retro_mmus_883, retro_mmus_918, retro_mmus_932, retro_mmus_940, retro_mmus_957, retro_mmus_993, retro_mmus_998,
Pan troglodytes	ENSPTRG00000005728	1 retrocopy	retro_ptro_66,
Rattus norvegicus	ENSRNOG00000000957	13 retrocopies	retro_rnor_227, retro_rnor_298, retro_rnor_319, retro_rnor_329, retro_rnor_330, retro_rnor_333, retro_rnor_365, retro_rnor_366, retro_rnor_416, retro_rnor_5, retro_rnor_79, retro_rnor_81, retro_rnor_82,
Sarcophilus harrisii	ENSSHAG00000000845	11 retrocopies	retro_shar_224, retro_shar_446, retro_shar_499, retro_shar_531, retro_shar_534, retro_shar_601, retro_shar_664, retro_shar_67, retro_shar_683, retro_shar_729, retro_shar_757,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	2.82 RPM
CEU_NA11843	2.67 RPM
CEU_NA11930	2.48 RPM
CEU_NA12004	1.29 RPM
CEU_NA12400	2.10 RPM
CEU_NA12751	1.04 RPM
CEU_NA12760	2.25 RPM
CEU_NA12827	2.78 RPM
CEU_NA12872	1.22 RPM
CEU_NA12873	2.58 RPM
FIN_HG00183	2.61 RPM
FIN_HG00277	2.37 RPM
FIN_HG00315	1.41 RPM
FIN_HG00321	1.18 RPM
FIN_HG00328	1.47 RPM
FIN_HG00338	1.72 RPM
FIN_HG00349	1.37 RPM
FIN_HG00375	1.64 RPM
FIN_HG00377	1.76 RPM
FIN_HG00378	1.40 RPM
GBR_HG00099	1.86 RPM
GBR_HG00111	1.87 RPM
GBR_HG00114	2.05 RPM
GBR_HG00119	1.27 RPM
GBR_HG00131	1.26 RPM
GBR_HG00133	1.33 RPM
GBR_HG00134	1.46 RPM
GBR_HG00137	2.75 RPM
GBR_HG00142	2.08 RPM
GBR_HG00143	1.95 RPM
TSI_NA20512	2.77 RPM
TSI_NA20513	1.09 RPM
TSI_NA20518	1.36 RPM
TSI_NA20532	2.38 RPM
TSI_NA20538	1.93 RPM
TSI_NA20756	1.51 RPM
TSI_NA20765	1.16 RPM
TSI_NA20771	2.01 RPM
TSI_NA20786	0.84 RPM
TSI_NA20798	1.37 RPM
YRI_NA18870	1.52 RPM
YRI_NA18907	1.42 RPM
YRI_NA18916	1.09 RPM
YRI_NA19093	1.54 RPM
YRI_NA19099	1.38 RPM
YRI_NA19114	1.28 RPM
YRI_NA19118	2.55 RPM
YRI_NA19213	0.86 RPM
YRI_NA19214	0.76 RPM
YRI_NA19223	1.49 RPM

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Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).